X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e1fd5721ebd38c25f525ace51f0df71c7db43bf5;hb=refs%2Fheads%2FJAL-4152-typed-singleton-provider;hp=9574e7e825c8f03acbe8d8110ad061e51496dd1e;hpb=7dcec14f584c3b4fc95e316e3d91e7d452889e5c;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 9574e7e..e1fd572 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,6 +20,11 @@ */ package jalview.bin; +import java.util.Locale; + +import java.awt.GraphicsEnvironment; +import java.awt.Color; + import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -45,17 +50,24 @@ import java.util.logging.Level; import java.util.logging.Logger; import javax.swing.JOptionPane; +import javax.swing.SwingUtilities; import javax.swing.UIManager; import javax.swing.UIManager.LookAndFeelInfo; +import com.formdev.flatlaf.FlatLightLaf; +import com.formdev.flatlaf.util.SystemInfo; import com.threerings.getdown.util.LaunchUtil; //import edu.stanford.ejalbert.launching.IBrowserLaunching; import groovy.lang.Binding; import groovy.util.GroovyScriptEngine; +import jalview.api.AlignCalcWorkerI; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; import jalview.gui.Desktop; +import jalview.gui.Preferences; import jalview.gui.PromptUserConfig; import jalview.io.AppletFormatAdapter; import jalview.io.BioJsHTMLOutput; @@ -93,9 +105,30 @@ import jalview.ws.jws2.Jws2Discoverer; * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements ApplicationSingletonI { - static + // for testing those nasty messages you cannot ever find. + // static + // { + // System.setOut(new PrintStream(new ByteArrayOutputStream()) + // { + // @Override + // public void println(Object o) + // { + // if (o != null) + // { + // System.err.println(o); + // } + // } + // + // }); + // } + public static Jalview getInstance() + { + return ApplicationSingletonProvider.getInstance(Jalview.class); + } + + private Jalview() { Platform.getURLCommandArguments(); Platform.addJ2SDirectDatabaseCall("https://www.jalview.org"); @@ -104,18 +137,47 @@ public class Jalview Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk"); } - /* - * singleton instance of this class - */ - private static Jalview instance; + + private boolean headless; private Desktop desktop; - public static AlignFrame currentAlignFrame; + public AlignFrame currentAlignFrame; + + public String appletResourcePath; + + public String j2sAppletID; + + private boolean noCalculation, noMenuBar, noStatus; + + private boolean noAnnotation; + + public boolean getStartCalculations() + { + return !noCalculation; + } + + public boolean getAllowMenuBar() + { + return !noMenuBar; + } + + public boolean getShowStatus() + { + return !noStatus; + } + + public boolean getShowAnnotation() + { + return !noAnnotation; + } static { - if (!Platform.isJS()) + if (Platform.isJS()) + { + Platform.getURLCommandArguments(); + } else /** * Java only * @@ -200,10 +262,7 @@ public class Jalview } - public static Jalview getInstance() - { - return instance; - } + private final static boolean doPlatformLogging = false; /** * main class for Jalview application @@ -213,50 +272,17 @@ public class Jalview */ public static void main(String[] args) { - // setLogging(); // BH - for event debugging in JavaScript - instance = new Jalview(); - instance.doMain(args); - } - - private static void logClass(String name) - { - // BH - for event debugging in JavaScript - ConsoleHandler consoleHandler = new ConsoleHandler(); - consoleHandler.setLevel(Level.ALL); - Logger logger = Logger.getLogger(name); - logger.setLevel(Level.ALL); - logger.addHandler(consoleHandler); - } - - @SuppressWarnings("unused") - private static void setLogging() - { - - /** - * @j2sIgnore - * - */ + if (doPlatformLogging) { - System.out.println("not in js"); + Platform.startJavaLogging(); } - // BH - for event debugging in JavaScript (Java mode only) - if (!Platform.isJS()) - /** - * Java only - * - * @j2sIgnore - */ - { - Logger.getLogger("").setLevel(Level.ALL); - logClass("java.awt.EventDispatchThread"); - logClass("java.awt.EventQueue"); - logClass("java.awt.Component"); - logClass("java.awt.focus.Component"); - logClass("java.awt.focus.DefaultKeyboardFocusManager"); - } + getInstance().doMain(args); } + + + /** * @param args @@ -264,11 +290,17 @@ public class Jalview void doMain(String[] args) { - if (!Platform.isJS()) + boolean isJS = Platform.isJS(); + if (!isJS) { System.setSecurityManager(null); } + /* + * @j2sNative J2S.db._DirectDatabaseCalls["compbio.dundee.ac.uk"]=null; + * @j2sNative J2S.db._DirectDatabaseCalls["jalview.org"]=null; + * + */ System.out .println("Java version: " + System.getProperty("java.version")); System.out.println("Java Home: " + System.getProperty("java.home")); @@ -292,48 +324,65 @@ public class Jalview } // report Jalview version - Cache.loadBuildProperties(true); + Cache.getInstance().loadBuildProperties(true); ArgsParser aparser = new ArgsParser(args); - boolean headless = false; + headless = false; String usrPropsFile = aparser.getValue("props"); Cache.loadProperties(usrPropsFile); // must do this before - if (usrPropsFile != null) + boolean allowServices = true; + + if (isJS) { - System.out.println( - "CMD [-props " + usrPropsFile + "] executed successfully!"); + j2sAppletID = Platform.getAppID(null); + Preferences.setAppletDefaults(); + Cache.loadProperties(usrPropsFile); // again, because we + // might be changing defaults here? + appletResourcePath = (String) aparser.getAppletValue("resourcepath", + null, true); } - if (!Platform.isJS()) + else /** * Java only * * @j2sIgnore */ { + if (usrPropsFile != null) + { + System.out.println( + "CMD [-props " + usrPropsFile + "] executed successfully!"); + } if (aparser.contains("help") || aparser.contains("h")) { showUsage(); System.exit(0); } + // BH note: Only -nodisplay is official; others are deprecated? if (aparser.contains("nodisplay") || aparser.contains("nogui") - || aparser.contains("headless")) + || aparser.contains("headless") + || GraphicsEnvironment.isHeadless()) { - System.setProperty("java.awt.headless", "true"); + if (!isJS) { + // BH Definitely not a good idea in JavaScript; + // probably should not be here for Java, either. + System.setProperty("java.awt.headless", "true"); + } headless = true; } // anything else! // allow https handshakes to download intermediate certs if necessary System.setProperty("com.sun.security.enableAIAcaIssuers", "true"); - - final String jabawsUrl = aparser.getValue("jabaws"); - if (jabawsUrl != null) + final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS); + allowServices = !("none".equals(jabawsUrl)); + if (allowServices && jabawsUrl != null) { try { - Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl); System.out.println( "CMD [-jabaws " + jabawsUrl + "] executed successfully!"); } catch (MalformedURLException e) @@ -344,7 +393,7 @@ public class Jalview } } - String defs = aparser.getValue("setprop"); + String defs = aparser.getValue(ArgsParser.SETPROP); while (defs != null) { int p = defs.indexOf('='); @@ -355,13 +404,10 @@ public class Jalview else { System.out.println("Executing setprop argument: " + defs); - if (Platform.isJS()) + if (isJS) { Cache.setProperty(defs.substring(0, p), defs.substring(p + 1)); } - // DISABLED FOR SECURITY REASONS - // TODO: add a property to allow properties to be overriden by cli args - // Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); } defs = aparser.getValue("setprop"); } @@ -372,7 +418,6 @@ public class Jalview } System.setProperty("http.agent", "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); - try { Console.initLogger(); @@ -392,16 +437,16 @@ public class Jalview * configure 'full' SO model if preferences say to, else use the default (full SO) * - as JS currently doesn't have OBO parsing, it must use 'Lite' version */ - boolean soDefault = !Platform.isJS(); + boolean soDefault = !isJS; if (Cache.getDefault("USE_FULL_SO", soDefault)) { - SequenceOntologyFactory.setInstance(new SequenceOntology()); + SequenceOntologyFactory.setSequenceOntology(new SequenceOntology()); } if (!headless) { Desktop.nosplash = aparser.contains("nosplash"); - desktop = new Desktop(); + desktop = Desktop.getInstance(); desktop.setInBatchMode(true); // indicate we are starting up try @@ -424,14 +469,22 @@ public class Jalview desktop.setVisible(true); - if (!Platform.isJS()) + if (isJS) + { + Cache.setProperty("SHOW_JWS2_SERVICES", "false"); + } + if (allowServices && !aparser.contains("nowebservicediscovery")) + { + desktop.startServiceDiscovery(); + } + + if (!isJS) /** * Java only * * @j2sIgnore */ { - /** * Check to see that the JVM version being run is suitable for the Java * version this Jalview was compiled for. Popup a warning if not. @@ -459,11 +512,6 @@ public class Jalview null, options, options[0]); } } - - if (!aparser.contains("nowebservicediscovery")) - { - desktop.startServiceDiscovery(); - } if (!aparser.contains("nousagestats")) { startUsageStats(desktop); @@ -530,45 +578,120 @@ public class Jalview + ") may lead to problems. This installation of Jalview should be used with Java " + LaunchUtils.getJavaCompileVersion() + "."); } + parseArguments(aparser, true); + } + + /** + * Parse all command-line String[] arguments as well as all JavaScript-derived + * parameters from Info. + * + * We allow for this method to be run from JavaScript. Basically allowing + * simple scripting. + * + * @param aparser + * @param isStartup + */ + public void parseArguments(ArgsParser aparser, boolean isStartup) + { - // Move any new getdown-launcher-new.jar into place over old - // getdown-launcher.jar - String appdirString = System.getProperty("getdownappdir"); - if (appdirString != null && appdirString.length() > 0) + String groovyscript = null; // script to execute after all loading is + boolean isJS = Platform.isJS(); + if (!isJS) + /** @j2sIgnore */ { - final File appdir = new File(appdirString); - new Thread() + // Move any new getdown-launcher-new.jar into place over old + // getdown-launcher.jar + String appdirString = System.getProperty("getdownappdir"); + if (appdirString != null && appdirString.length() > 0) { - @Override - public void run() + final File appdir = new File(appdirString); + new Thread() { - LaunchUtil.upgradeGetdown( - new File(appdir, "getdown-launcher-old.jar"), - new File(appdir, "getdown-launcher.jar"), - new File(appdir, "getdown-launcher-new.jar")); - } - }.start(); - } + @Override + public void run() + { + LaunchUtil.upgradeGetdown( + new File(appdir, "getdown-launcher-old.jar"), + new File(appdir, "getdown-launcher.jar"), + new File(appdir, "getdown-launcher-new.jar")); + } + }.start(); + } - String file = null, data = null; - FileFormatI format = null; - DataSourceType protocol = null; - FileLoader fileLoader = new FileLoader(!headless); + // completed one way or another + // extract groovy argument and execute if necessary + groovyscript = aparser.getValue("groovy", true); + } - String groovyscript = null; // script to execute after all loading is - // completed one way or another - // extract groovy argument and execute if necessary - groovyscript = aparser.getValue("groovy", true); - file = aparser.getValue("open", true); + String file = aparser.getValue("open", true); - if (file == null && desktop == null) + if (!isJS && file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } + setDisplayParameters(aparser); + + // time to open a file. long progress = -1; + DataSourceType protocol = null; + FileLoader fileLoader = new FileLoader(!headless); + FileFormatI format = null; // Finally, deal with the remaining input data. - if (file != null) + AlignFrame af = null; + + JalviewJSApp jsApp = (isJS ? new JalviewJSApp(this, aparser) : null); + + if (file == null) + { + if (isJS) + { + // JalviewJS allows sequence1 sequence2 .... + + } + else if (!headless && Cache.getDefault("SHOW_STARTUP_FILE", true)) + /** + * Java only + * + * @j2sIgnore + */ + { + file = Cache.getDefault("STARTUP_FILE", + Cache.getDefault("www.jalview.org", "https://www.jalview.org") + + "/examples/exampleFile_2_7.jvp"); + if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar") + || file.equals( + "http://www.jalview.org/examples/exampleFile_2_7.jar")) + { + file.replace("http:", "https:"); + // hardwire upgrade of the startup file + file.replace("_2_3", "_2_7"); + file.replace("2_7.jar", "2_7.jvp"); + // and remove the stale setting + Cache.removeProperty("STARTUP_FILE"); + } + + protocol = AppletFormatAdapter.checkProtocol(file); + + if (file.endsWith(".jar")) + { + format = FileFormat.Jalview; + } + else + { + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e) + { + // TODO what? + } + } + + af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); + } + } + else { if (!headless) { @@ -599,312 +722,421 @@ public class Jalview } } + // JS Only argument to provide a format parameter to specify what format to use + String fileFormat = (isJS + ? (String) aparser.getAppletValue("format", null, true) + : null); protocol = AppletFormatAdapter.checkProtocol(file); try { - format = new IdentifyFile().identify(file, protocol); + format = (fileFormat != null + ? FileFormats.getInstance().forName(fileFormat) + : null); + if (format == null) + { + format = new IdentifyFile().identify(file, protocol); + } } catch (FileFormatException e1) { // TODO ? } - AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, + af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol, format); if (af == null) { - System.out.println("error"); + System.out.println("jalview error - AlignFrame was not created"); } else { - setCurrentAlignFrame(af); - data = aparser.getValue("colour", true); - if (data != null) + + // JalviewLite interface for JavaScript allows second file open + String file2 = aparser.getValue(ArgsParser.OPEN2, true); + if (file2 != null) { - data.replaceAll("%20", " "); - - ColourSchemeI cs = ColourSchemeProperty.getColourScheme( - af.getViewport(), af.getViewport().getAlignment(), data); - - if (cs != null) + protocol = AppletFormatAdapter.checkProtocol(file2); + try { - System.out.println( - "CMD [-color " + data + "] executed successfully!"); + format = new IdentifyFile().identify(file2, protocol); + } catch (FileFormatException e1) + { + // TODO ? } - af.changeColour(cs); - } - - // Must maintain ability to use the groups flag - data = aparser.getValue("groups", true); - if (data != null) - { - af.parseFeaturesFile(data, - AppletFormatAdapter.checkProtocol(data)); - // System.out.println("Added " + data); - System.out.println( - "CMD groups[-" + data + "] executed successfully!"); - } - data = aparser.getValue("features", true); - if (data != null) - { - af.parseFeaturesFile(data, - AppletFormatAdapter.checkProtocol(data)); - // System.out.println("Added " + data); - System.out.println( - "CMD [-features " + data + "] executed successfully!"); - } - - data = aparser.getValue("annotations", true); - if (data != null) - { - af.loadJalviewDataFile(data, null, null, null); - // System.out.println("Added " + data); - System.out.println( - "CMD [-annotations " + data + "] executed successfully!"); - } - // set or clear the sortbytree flag. - if (aparser.contains("sortbytree")) - { - af.getViewport().setSortByTree(true); - if (af.getViewport().getSortByTree()) + AlignFrame af2 = new FileLoader(!headless) + .LoadFileWaitTillLoaded(file2, protocol, format); + if (af2 == null) { - System.out.println("CMD [-sortbytree] executed successfully!"); + System.out.println("error"); } - } - if (aparser.contains("no-annotation")) - { - af.getViewport().setShowAnnotation(false); - if (!af.getViewport().isShowAnnotation()) + else { - System.out.println("CMD no-annotation executed successfully!"); + AlignViewport.openLinkedAlignmentAs(af, + af.getViewport().getAlignment(), + af2.getViewport().getAlignment(), "", + AlignViewport.SPLIT_FRAME); + System.out.println( + "CMD [-open2 " + file2 + "] executed successfully!"); } } - if (aparser.contains("nosortbytree")) + // af is loaded - so set it as current frame + setCurrentAlignFrame(af); + + setFrameDependentProperties(aparser, af); + + if (isJS) { - af.getViewport().setSortByTree(false); - if (!af.getViewport().getSortByTree()) - { - System.out - .println("CMD [-nosortbytree] executed successfully!"); - } + jsApp.initFromParams(af); } - data = aparser.getValue("tree", true); - if (data != null) + else + /** + * Java only + * + * @j2sIgnore + */ { - try + if (groovyscript != null) { - System.out.println( - "CMD [-tree " + data + "] executed successfully!"); - NewickFile nf = new NewickFile(data, - AppletFormatAdapter.checkProtocol(data)); - af.getViewport() - .setCurrentTree(af.showNewickTree(nf, data).getTree()); - } catch (IOException ex) - { - System.err.println("Couldn't add tree " + data); - ex.printStackTrace(System.err); + // Execute the groovy script after we've done all the rendering + // stuff + // and before any images or figures are generated. + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); + groovyscript = null; } } - // TODO - load PDB structure(s) to alignment JAL-629 - // (associate with identical sequence in alignment, or a specified - // sequence) - if (groovyscript != null) - { - // Execute the groovy script after we've done all the rendering stuff - // and before any images or figures are generated. - System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, af); - System.out.println("CMD groovy[" + groovyscript - + "] executed successfully!"); - groovyscript = null; + if (!isJS || !isStartup) { + createOutputFiles(aparser, format); } - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) - { - String outputFormat = aparser.nextValue(); - file = aparser.nextValue(); + } + if (headless) + { + af.getViewport().getCalcManager().shutdown(); + } + } + // extract groovy arguments before anything else. + // Once all other stuff is done, execute any groovy scripts (in order) + if (!isJS && groovyscript != null) + { + if (Cache.groovyJarsPresent()) + { + // TODO: DECIDE IF THIS SECOND PASS AT GROOVY EXECUTION IS STILL REQUIRED !! + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); - if (outputFormat.equalsIgnoreCase("png")) - { - af.createPNG(new File(file)); - imageName = (new File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("svg")) - { - File imageFile = new File(file); - imageName = imageFile.getName(); - af.createSVG(imageFile); - System.out.println("Creating SVG image: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("html")) - { - File imageFile = new File(file); - imageName = imageFile.getName(); - HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); - htmlSVG.exportHTML(file); + } + else + { + System.err.println( + "Sorry. Groovy Support is not available, so ignoring the provided groovy script " + + groovyscript); + } + } - System.out.println("Creating HTML image: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("biojsmsa")) - { - if (file == null) - { - System.err.println("The output html file must not be null"); - return; - } - try - { - BioJsHTMLOutput.refreshVersionInfo( - BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); - } catch (URISyntaxException e) - { - e.printStackTrace(); - } - BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); - bjs.exportHTML(file); - System.out - .println("Creating BioJS MSA Viwer HTML file: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("imgMap")) - { - af.createImageMap(new File(file), imageName); - System.out.println("Creating image map: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("eps")) - { - File outputFile = new File(file); - System.out.println( - "Creating EPS file: " + outputFile.getAbsolutePath()); - af.createEPS(outputFile); - continue; - } - FileFormatI outFormat = null; - try - { - outFormat = FileFormats.getInstance().forName(outputFormat); - } catch (Exception formatP) - { - System.out.println("Couldn't parse " + outFormat - + " as a valid Jalview format string."); - } - if (outFormat != null) - { - if (!outFormat.isWritable()) - { - System.out.println( - "This version of Jalview does not support alignment export as " - + outputFormat); - } - else - { - af.saveAlignment(file, outFormat); - if (af.isSaveAlignmentSuccessful()) - { - System.out.println("Written alignment in " - + outFormat.getName() + " format to " + file); - } - else - { - System.out.println("Error writing file " + file + " in " - + outFormat.getName() + " format!!"); - } - } - } + // and finally, turn off batch mode indicator - if the desktop still exists + if (desktop != null) + { + if (progress != -1) + { + desktop.setProgressBar(null, progress); + } + desktop.setInBatchMode(false); + } + + if (jsApp != null) { + jsApp.callInitCallback(); + } + } + + /** + * Set general display parameters irrespective of file loading or headlessness. + * + * @param aparser + */ + private void setDisplayParameters(ArgsParser aparser) + { + if (aparser.contains(ArgsParser.NOMENUBAR)) + { + noMenuBar = true; + System.out.println("CMD [nomenu] executed successfully!"); + } - } + if (aparser.contains(ArgsParser.NOSTATUS)) + { + noStatus = true; + System.out.println("CMD [nostatus] executed successfully!"); + } - while (aparser.getSize() > 0) - { - System.out.println("Unknown arg: " + aparser.nextValue()); - } - } + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) + { + noAnnotation = true; + System.out.println("CMD no-annotation executed successfully!"); + } + if (aparser.contains(ArgsParser.NOCALCULATION)) + { + noCalculation = true; + System.out.println("CMD [nocalculation] executed successfully!"); } - AlignFrame startUpAlframe = null; - // We'll only open the default file if the desktop is visible. - // And the user - // //////////////////// + } - if (!Platform.isJS() && !headless && file == null - && Cache.getDefault("SHOW_STARTUP_FILE", true)) - /** - * Java only - * - * @j2sIgnore - */ + private void setFrameDependentProperties(ArgsParser aparser, + AlignFrame af) + { + String data = aparser.getValue(ArgsParser.COLOUR, true); + if (data != null) { - file = Cache.getDefault("STARTUP_FILE", - Cache.getDefault("www.jalview.org", "https://www.jalview.org") - + "/examples/exampleFile_2_7.jvp"); - if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar") - || file.equals( - "http://www.jalview.org/examples/exampleFile_2_7.jar")) + data.replaceAll("%20", " "); + + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); + + if (cs != null) { - file.replace("http:", "https:"); - // hardwire upgrade of the startup file - file.replace("_2_3", "_2_7"); - file.replace("2_7.jar", "2_7.jvp"); - // and remove the stale setting - Cache.removeProperty("STARTUP_FILE"); + System.out.println( + "CMD [-color " + data + "] executed successfully!"); } + af.changeColour(cs); + } - protocol = AppletFormatAdapter.checkProtocol(file); + // Must maintain ability to use the groups flag + data = aparser.getValue(ArgsParser.GROUPS, true); + if (data != null) + { + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println( + "CMD groups[-" + data + "] executed successfully!"); + } + data = aparser.getValue(ArgsParser.FEATURES, true); + if (data != null) + { + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println( + "CMD [-features " + data + "] executed successfully!"); + } + data = aparser.getValue(ArgsParser.ANNOTATIONS, true); + if (data != null) + { + af.loadJalviewDataFile(data, null, null, null); + // System.out.println("Added " + data); + System.out.println( + "CMD [-annotations " + data + "] executed successfully!"); + } - if (file.endsWith(".jar")) + // JavaScript feature + + if (aparser.contains(ArgsParser.SHOWOVERVIEW)) + { + af.overviewMenuItem_actionPerformed(null); + System.out.println("CMD [showoverview] executed successfully!"); + } + + // set or clear the sortbytree flag. + if (aparser.contains(ArgsParser.SORTBYTREE)) + { + af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) { - format = FileFormat.Jalview; + System.out.println("CMD [-sortbytree] executed successfully!"); } - else + } + + boolean doUpdateAnnotation = false; + /** + * we do this earlier in JalviewJS because of a complication with + * SHOWOVERVIEW + * + * For now, just fixing this in JalviewJS. + * + * + * @j2sIgnore + * + */ + { + if (noAnnotation) { - try - { - format = new IdentifyFile().identify(file, protocol); - } catch (FileFormatException e) + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) { - // TODO what? + doUpdateAnnotation = true; } } - startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, - format); - // extract groovy arguments before anything else. } - // Once all other stuff is done, execute any groovy scripts (in order) - if (groovyscript != null) + if (aparser.contains(ArgsParser.NOSORTBYTREE)) { - if (Cache.groovyJarsPresent()) + af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) { - System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, startUpAlframe); + doUpdateAnnotation = true; + System.out + .println("CMD [-nosortbytree] executed successfully!"); } - else + } + if (doUpdateAnnotation) + { // BH 2019.07.24 + af.setMenusForViewport(); + af.alignPanel.updateLayout(); + } + + data = aparser.getValue(ArgsParser.TREE, true); + if (data != null) + { + try { - System.err.println( - "Sorry. Groovy Support is not available, so ignoring the provided groovy script " - + groovyscript); + NewickFile nf = new NewickFile(data, + AppletFormatAdapter.checkProtocol(data)); + af.getViewport() + .setCurrentTree(af.showNewickTree(nf, data).getTree()); + System.out.println( + "CMD [-tree " + data + "] executed successfully!"); + } catch (IOException ex) + { + System.err.println("Couldn't add tree " + data); + ex.printStackTrace(System.err); } } - // and finally, turn off batch mode indicator - if the desktop still exists - if (desktop != null) + // TODO - load PDB structure(s) to alignment JAL-629 + // (associate with identical sequence in alignment, or a specified + // sequence) + + } + + /** + * Writes an output file for each format (if any) specified in the + * command-line arguments. Supported formats are currently + * + * A format parameter should be followed by a parameter specifying the output + * file name. {@code imgMap} parameters should follow those for the + * corresponding alignment image output. + * + * @param aparser + * @param format + */ + private void createOutputFiles(ArgsParser aparser, FileFormatI format) + { + // logic essentially the same as 2.11.2/2.11.3 but uses a switch instead + AlignFrame af = currentAlignFrame; + while (aparser.getSize() >= 2) { - if (progress != -1) + String outputFormat = aparser.nextValue(); + File imageFile; + String fname; + switch (outputFormat.toLowerCase(Locale.ROOT)) { - desktop.setProgressBar(null, progress); + case "png": + imageFile = new File(aparser.nextValue()); + af.createPNG(imageFile); + System.out.println( + "Creating PNG image: " + imageFile.getAbsolutePath()); + continue; + case "svg": + imageFile = new File(aparser.nextValue()); + af.createSVG(imageFile); + System.out.println( + "Creating SVG image: " + imageFile.getAbsolutePath()); + continue; + case "eps": + imageFile = new File(aparser.nextValue()); + System.out.println( + "Creating EPS file: " + imageFile.getAbsolutePath()); + af.createEPS(imageFile); + continue; + case "biojsmsa": + fname = new File(aparser.nextValue()).getAbsolutePath(); + try + { + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(fname); + System.out.println("Creating BioJS MSA Viwer HTML file: " + fname); + continue; + case "html": + fname = new File(aparser.nextValue()).getAbsolutePath(); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); + htmlSVG.exportHTML(fname); + System.out.println("Creating HTML image: " + fname); + continue; + case "imgmap": + imageFile = new File(aparser.nextValue()); + af.alignPanel.makePNGImageMap(imageFile, "unnamed.png"); + System.out.println( + "Creating image map: " + imageFile.getAbsolutePath()); + continue; + default: + // fall through - try to parse as an alignment data export format + FileFormatI outFormat = null; + try + { + outFormat = FileFormats.getInstance().forName(outputFormat); + } catch (Exception formatP) + { + } + if (outFormat == null) + { + System.out.println("Couldn't parse " + outputFormat + + " as a valid Jalview format string."); + continue; + } + if (!outFormat.isWritable()) + { + System.out.println( + "This version of Jalview does not support alignment export as " + + outputFormat); + continue; + } + // record file as it was passed to Jalview so it is recognisable to the CLI + // caller + String file; + fname = new File(file = aparser.nextValue()).getAbsolutePath(); + // JBPNote - yuck - really wish we did have a bean returned from this which gave + // success/fail like before ! + af.saveAlignment(fname, outFormat); + if (!af.isSaveAlignmentSuccessful()) + { + System.out.println("Written alignment in " + outputFormat + + " format to " + file); + continue; + } + else + { + System.out.println("Error writing file " + file + " in " + + outputFormat + " format!!"); + } } - desktop.setInBatchMode(false); + } + // ??? Should report - 'ignoring' extra args here... + while (aparser.getSize() > 0) + { + System.out.println("Ignoring extra argument: " + aparser.nextValue()); } } private static void setLookAndFeel() { - // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or - // "mac" + // property laf = "crossplatform", "system", "gtk", "metal", "nimbus", + // "mac" or "flat" // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac, // try Quaqua/Vaqua. String lafProp = System.getProperty("laf"); @@ -956,6 +1188,13 @@ public class Jalview Console.error("Could not set requested laf=" + laf); } break; + case "flat": + lafSet = setFlatLookAndFeel(); + if (!lafSet) + { + Console.error("Could not set requested laf=" + laf); + } + break; case "quaqua": lafSet = setQuaquaLookAndFeel(); if (!lafSet) @@ -1076,6 +1315,44 @@ public class Jalview "javax.swing.plaf.nimbus.NimbusLookAndFeel", false); } + private static boolean setFlatLookAndFeel() + { + boolean set = setSpecificLookAndFeel("flatlaf light", + "com.formdev.flatlaf.FlatLightLaf", false); + if (set) + { + if (Platform.isMac()) + { + System.setProperty("apple.laf.useScreenMenuBar", "true"); + System.setProperty("apple.awt.application.name", + ChannelProperties.getProperty("app_name")); + System.setProperty("apple.awt.application.appearance", "system"); + if (SystemInfo.isMacFullWindowContentSupported + && Desktop.getInstance() != null) + { + Desktop.getInstance().getRootPane() + .putClientProperty("apple.awt.fullWindowContent", true); + Desktop.getInstance().getRootPane() + .putClientProperty("apple.awt.transparentTitleBar", true); + } + + SwingUtilities.invokeLater(() -> { + FlatLightLaf.setup(); + }); + } + + UIManager.put("TabbedPane.showTabSeparators", true); + UIManager.put("TabbedPane.tabSeparatorsFullHeight", true); + UIManager.put("TabbedPane.tabsOverlapBorder", true); + // UIManager.put("TabbedPane.hasFullBorder", true); + UIManager.put("TabbedPane.tabLayoutPolicy", "scroll"); + UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded"); + UIManager.put("TabbedPane.smoothScrolling", true); + UIManager.put("TabbedPane.tabWidthMode", "compact"); + UIManager.put("TabbedPane.selectedBackground", Color.white); + } + return set; + } private static boolean setQuaquaLookAndFeel() { return setSpecificLookAndFeel("quaqua", @@ -1096,12 +1373,16 @@ public class Jalview System.setProperty("com.apple.mrj.application.apple.menu.about.name", ChannelProperties.getProperty("app_name")); System.setProperty("apple.laf.useScreenMenuBar", "true"); + /* + * broken native LAFs on (ARM?) macbooks set = setQuaquaLookAndFeel(); if ((!set) || !UIManager.getLookAndFeel().getClass().toString() .toLowerCase(Locale.ROOT).contains("quaqua")) { set = setVaquaLookAndFeel(); } + */ + set = setFlatLookAndFeel(); return set; } @@ -1153,7 +1434,7 @@ public class Jalview /** * start a User Config prompt asking if we can log usage statistics. */ - PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop, + PromptUserConfig prompter = new PromptUserConfig(Desktop.getDesktopPane(), "USAGESTATS", "Jalview Usage Statistics", "Do you want to help make Jalview better by enabling " + "the collection of usage statistics with Google Analytics ?" @@ -1315,8 +1596,8 @@ public class Jalview } /** - * Quit method delegates to Desktop.quit - unless running in headless mode - * when it just ends the JVM + * Quit method delegates to Desktop.quit - unless running in headless mode when + * it just ends the JVM */ public void quit() { @@ -1332,11 +1613,30 @@ public class Jalview public static AlignFrame getCurrentAlignFrame() { - return Jalview.currentAlignFrame; + return Jalview.getInstance().currentAlignFrame; } public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) { - Jalview.currentAlignFrame = currentAlignFrame; + Jalview.getInstance().currentAlignFrame = currentAlignFrame; + } + + public void notifyWorker(AlignCalcWorkerI worker, String status) + { + // System.out.println("Jalview worker " + worker.getClass().getSimpleName() + // + " " + status); + } + + + private static boolean isInteractive = true; + + public static boolean isInteractive() + { + return isInteractive; + } + + public static void setInteractive(boolean tf) + { + isInteractive = tf; } }